Genome orientation, convention to begin at one end of a chromosome

Question

[Stingery]

When working with genetic data obtained from genotyping or sequencing, one finds the generated data files in a specific orientation per chromosome. That is, each chromosome is defined with one of its ends as the 'start' of the sequence. For example, consider a VCF file for a given chromosome. In any study, the same chromosome will start at the same end of the chromosome (i.e. not in reverse orientation).

My questions:

Where in the process from DNA extraction to datafile generation is this orientation determined?

Where is this convention (I assume it is a convention) listed?

Answer 1

[Devon Ryan]

The start is defined when the reference genome is made. For the human genome, this is the p arm of a chromosome. For other genomes it may be random or follow some other arbitrary rule.